Table 2.

Strengths and limitations of sequencing strategy in the indoor microbiome study.

Sequencing strategy	Sequencing platform	Sequencing statistics	Strengths	Limitations
Amplicon sequencing	Illumina MiSeq, NextSeq	Read length: 2 × 100 bp–2 × 250 bp Sequencing depth: 30,000–100,000 reads	1.Cheap 2.High nucleotide sequencing accuracy 3.Mature reference database and analyzing pipelines 4.Require a low amount of sample and DNA	1.Only a sub-region of the amplicon genes is sequenced, such as V1–V2, V3–V5, and V6–V9 region of the 16S ribosomal RNA 2.Low taxonomic resolution (generally at the genus or above levels) 3.Sequencing bias during the template annealing process in the amplification process 4.No accurate functional inference
	PacBio Sequel, Sequel II, Nanopore MinION	Read length: >1500 bp Sequencing depth: 4000–10,000 reads	1.Long sequencing reads, enable species-level taxonomic inference 2.Circular consensus technique can improve the nucleotide sequencing accuracy to >99.9%	1. More expansive than second-generation amplicon sequencing 2. Low sequencing depth and output (limit in detecting low-frequency variants) 3. No accurate functional inference
Shotgun metagenomics sequencing	Illumina HiSeq, NovaSeq	Read length: 2 × 100 bp–2 × 250 bp Sequencing depth: 20–100 million reads	1.Species or strain level taxonomic inference 2.Functional inference of the whole catalog of microbial community	1.Require a high amount and high quality of sample and DNA 2.Long computational time require extensive computational resources to process gigabytes or even terabytes of data